[Joelib-devel] a trouble to match a new element : R

[Joerg K. W. <we...@in...>]

Dear NAJI,

1. radicals R are not supported directly.

2. You can not simply add a new element entry in the element table
joelib/data/plain/element.txt, because this type must be anywhere 
assigned and this is not the case at all.
Typically this is done by the SMARTS atom types (PATTY algorithm) in
joelib/data/plain/atomtype.txt
So, radicals are much more difficult, because electron counts are at the 
moment not supported by SMARTS matching and therefore also not for the 
PATTY algorithm. See also:
joelib/smarts/JOESmartsPattern.java
joelib/smarts/ParseSmart.java
joelib/smarts/Patty.java

3. Smiles does not recognize 'R'. So there exists still a request for 
this feature, but there they requested the R-groups analogue to the 
entries in SDF files. So, what is the standard here ?
http://sourceforge.net/tracker/index.php?func=detail&aid=970983&group_id=39708&atid=425970

I've increased the priority to 6.

Kind regards, Joerg

-- 
Dipl. Chem. Joerg K. Wegner
Center of Bioinformatics Tuebingen (ZBIT)
Department of Computer Architecture
Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071 29 78970
Fax: (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW:    http://www-ra.informatik.uni-tuebingen.de
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